- B similarity: E = (B_i - B_j)^2 / (kappa^2 B_i B_j), the symmetric Kullback-Leibler divergence of two
isotropic Gaussians (Murshudov et al. 2011), so sigma = kappa sqrt(B_i B_j) instead of a fixed 1.5-4.5 A^2.
kappa 0.1 / 0.133 / 0.2 / 0.3 for main-chain bonded / angle-related and side-chain pairs (REFMAC's logs list
sigma ~0.1 B for main-chain bonded pairs at B 11-140; the ratios are those of the old sigmas, which these
equal at B = 15). New class: atoms within 4 A that no bond or angle relates, waters and symmetry mates
included, kappa 0.5 (BuildBContacts, sharing the neighbour search with BuildRepulsions). CPU and GPU.
- The B factors' X-ray weight is balanced on its own (BalancedADPWeight: B-restraint over X-ray B-gradient on
the model with B shaken by 20%) instead of being a multiple of the positional weight; the ladder tries B held
and refined at that weight, the trajectory's B steps divide and multiply it by four, positional steps and the
final ladder leave it.
- Before each B-refining macro-cycle the overall isotropic B of the scale moves into the atoms and the
solvent's B (F_model unchanged), so the two do not drift against each other.
Tried and not kept: xyz and B as one L-BFGS vector (the B block scaled by its curvature, the positions by the
median X-ray curvature): no better than alternation with a memory per block on 12 starts (mean R-free 0.265
vs 0.262), worse on 7arr/7d98; a refit before each B step: no gain for +20-40% time.
Refinement battery MD starts, median R-free by the REFMAC 0-cycle scorer, previous commit -> this (REFMAC to
convergence): 5f6m x8 0.167 -> 0.167 (0.168), 8dqb x8 0.291 -> 0.294 (0.284), 7arr x4 0.270 -> 0.278 (0.311),
11if x4 0.245 -> 0.244 (0.251), 5reo x4 0.312 -> 0.258 (0.261: the ladder no longer keeps B held where B is the
model's largest error), 7d98 x4 0.342 -> 0.335 (0.361). Deposited models: unchanged (B stays held there).
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit ed292f35b482b696d81f71f1d97e0016ca05b144)
leonarski_f
bda90dbdd5
